Single genome analysis reveals genetic characteristics of Neuroadaptation across HIV-1 envelope

Edwin Kamau,Xiang‐Peng Kong ,Teresa H. Evering ,Charles B Farmer ,Martin Markowitz,Leslie St. Bernard

doi:10.1186/preaccept-1509273248119831

Abstract

BackgroundThe widespread use of highly effective, combination antiretroviral therapy (cART) has led to a significant reduction in the incidence of HIV-associated dementia (HAD). Despite these advances, the prevalence of HIV-1 associated neurocognitive disorders (HANDs) has been estimated at approximately 40%-50%. In the cART era, the majority of this disease burden is represented by asymptomatic neurocognitive impairment and mild neurocognitive disorder (ANI and MND respectively). Although less severe than HAD, these diagnoses carry with them substantial morbidity.ResultsIn this cross-sectional study, single genome amplification (SGA) was used to sequence 717 full-length HIV-1 envelope (env) clade B variants from the paired cerebrospinal fluid (CSF) and blood plasma samples of fifteen chronically infected HIV-positive individuals with normal neurocognitive performance (NCN), ANI and MND. Various degrees of compartmentalization were found across disease states and history of cART utilization. In individuals with compartmentalized virus, mean HIV-1 env population diversity was lower in the CSF than plasma-derived variants. Overall, mean V1V2 loop length was shorter in CSF-derived quasispecies when compared to contemporaneous plasma populations, and this was found to correlate with a lower mean number of N-linked glycosylation sites in this region. A number of discrete amino acid positions that correlate strongly with compartmentalization in the CSF were identified in both variable and constant regions of gp120 as well as in gp41. Correlated mutation analyses further identified that a subset of amino acid residues in these compartmentalization “hot spot” positions were strongly correlated with one another, suggesting they may play an important, definable role in the adaptation of viral variants to the CSF. Analysis of these hot spots in the context of a well-supported crystal structure of HIV-1 gp120 suggests mechanisms through which amino acid differences at the identified residues might contribute to viral compartmentalization in the CSF.ConclusionsThe detailed analyses of SGA-derived full length HIV-1 env from subjects with both normal neurocognitive performance and the most common HAND diagnoses in the cART era allow us to identify novel and confirm previously described HIV-1 env genetic determinants of neuroadaptation and relate potential motifs to HIV-1 env structure and function.

Highlights

The widespread use of highly effective, combination antiretroviral therapy has led to a significant reduction in the incidence of HIV-associated dementia (HAD)
We describe genetic features of HIV-1 env that correlate with the presence of viral variants in the cerebrospinal fluid (CSF) versus plasma, determine shared patterns of CNS compartmentalization of HIV-1 env in a cohort of individuals with chronic HIV-1 infection, reveal the existence of correlated mutation covariation across full length HIV-1 env and interpret these findings in the context of current knowledge of the structure of gp120
Clinical characteristics of the study groups We obtained clinical samples from fifteen individuals with chronic HIV-1 infection previously enrolled in the CNS HIV Antiretroviral Therapy Effects Research (CHARTER) study

Summary

Introduction

The widespread use of highly effective, combination antiretroviral therapy (cART) has led to a significant reduction in the incidence of HIV-associated dementia (HAD) Despite these advances, the prevalence of HIV-1 associated neurocognitive disorders (HANDs) has been estimated at approximately 40%-50%. The widespread use of highly effective combination antiretroviral therapy (cART) has led to a clear reduction in the incidence of HIV-associated dementia (HAD), one of the most severe manifestations of HIV-1 CNS infection [4]. Despite this decrease, HIV-1 associated neurocognitive disorders (HANDs) persist in the cART era [5], with an estimated prevalence of approximately 40-50% [6,7]. HIV-1 associated neurocognitive disorders less severe than frank dementia have been shown to be independently associated with an increased risk for mortality in those with HIV [10] and a recent study suggests the self-report of functional performance may underestimate symptomatic impairment in HAND [11]

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